1. Ontology Development and Usage for Protozoan Parasite Research John A. Miller and Alok Dhamanaskar Collaborators: Michael E. Cotterell, Chaitanya Guttula, Yung Long Li and Jessica C. Kissinger, University of Georgia. Jie Zheng and Christian J. Stoeckert, Jr., University of Pennsylvania. Tania Tudorache, Natasha Noy, Mark Musen, Stanford University Integrative Tools for Protozoan Parasite Research R01 GM093132 2012 NCBO Project Meeting Stanford University

2. Ontology Development and Usage for Protozoan Parasite Research: Aim 1 1.Support development of forms for isolate collections, phenotypes, and other metadata using a semantic framework based on OBO Foundry-compliant ontologies 1.Ontology for Biomedical Investigations (OBI) 2.Ontology for Parasite Lifecycle (OPL) 3.Collaborative ontology development with Web Protégé

3. Ontology Development and Usage for Protozoan Parasite Research: Aim 2 2.Development of a Framework for Semantic Annotations 1.Enrichment of the Ontology for Biomedical Investigations (OBI) 1.OBI: purl.obolibrary.org/obo/obi.owl 2.OBI-enriched-WS: obi-webservice.googlecode.com 3.OBI-WS: OBI Extended Web Services Ontology 2.Creation of Web Services / Processes for Protozoan Parasite Research 1.Phylip SOAP Web Service 2.Re-engineer REST Web Services for EuPathDB 3.Workflow: Sequence and Phylogenetic Analysis of Proteins 3.Semantic Annotation of Existing Web Services Using Ontologies 1.Using Semantic Annotations for WSDL (SAWSDL) for SOAP Services 2.Using Semantic Annotations for WADL for REST Services and Galaxy Tools 3.Demonstrating the effectiveness of using ontologies in applications

4. Ontology Development and Usage for Protozoan Parasite Research: Aim 3 3.Development of Web Services, Workflows and Data Integration Tools 1.Provision of Web Service Support for Galaxy 1.Tool 1: Web Service Extension for Galaxy: Galaxy WS-Extensions 2.Improved Automation through Semantics 1.Tool 2: Service Annotation: RadiantWeb 2.Tool 3: Service Discovery: LuminaWeb 3.Tool 4: Service Suggestion Engine: SSE Example from 2.2.3: Development of a Workflow

5. Choice of a Workflow System http://www.jboss.org/jbpm/components/eclipse-plugin/mainColumnParagraphs/00/imageBinary/Screenshot-1.png http://www.beilstein-institut.de/escec2007/proceedings/Snoep/images/ESCEC2007_10_03a.jpg I have heard that jBPM is very powerful, Taverna is very popular, but Galaxy is very easy to use. Workflow system for end user.

6. Find Services / Tools for My Workflow # = 2289 # = 28606 # = 393 #93 #354 #36 #0 Seems like a lot of services to look through ! I wonder if I missed any ? Total Services = 483 with maybe 1000s of operations Sequence Alignment Search Popular Web service Registries Tools available in Galaxy (461) + Tools in the Galaxy Tool-shed (232) Service Discovery

7. Find Input-Output Compatible S ervices I selected 2 of those operations, entered them in my workflow designer, but when I tested, it didn’t work. Type1 Type2 C BA ED BA Type1 Case 3 Require Data Mediation OutputInput Type Mismatch Input output Matching Problem

8. Connect the Newly Added Service into the Workflow Wish I could figure out which service operation(s) might fill the gap in my workflow. ? ? ? Workflow design / service composition Why can’t the computer make a suggestion?

9. Find Services / Tools Issues related to working with Web Services and Tools: For SOAP Web Services For REST Web Services and tools Web services are developed by different contributors Not developed to work with one another No standard naming conventions Text descriptions are inherently ambiguous

10. Find Services: Ontological Solutions We have formalized a methodology for enriching an Ontology with terms to support Web service annotation, Enriched the OBI ontology, by generating ~130 new terms to support annotation of 61 operations from 12 popular Web Services. <input name=“seq” /> WSDL for WUBLAST Web service Ontology provide a rich modeling framework, enable reuse of domain knowledge, facilitate community agreement, facilitates reasoning to ensure consistency. Ontologies

11. Find Services: Semantic Annotations RadiantWeb Annotation Tool Semantic Mark-up of Description Documents: What does it take ?

12. Find Input-Output Compatible Services and Connect Them The Service Suggestion Engine (SSE) is a semi-automatic workflow composition system that utilizes semantic annotations. What it does: Facilitates the construction and extension of workflows by providing suggestions to the user for the next step. It is capable of doing Forward Suggestions, Backward Suggestions and Bi-directional Suggestions. 1 2 ? ? 1 2 1 ? 2

13. Sample Use Case for SSE Find out more information about a protein sequence and its evolutionary relationships to other protein sequences. The user might be aware that he wants to first search a database for similar sequences, then perform multiple sequence alignment and finally perform phylogenetic analysis to construct phylogenetic trees. Web services already exist for each of the above. We utilize semantically annotated versions of their descriptions for our example.

14. How Ontologies can Help in Workflow Construction Step 2 Step 1 Step 3 Ranked out of 60 available Web service operations

15. Effectiveness of Ontological Annotations Average Precision, Recall and F-Measure for Different levels of Annotations Precision, Recall and F-Measure for each step in the workflow

16. How NCBO Enables this Work Editor: Protégé Has been vital for the Ontology Development aspect of our project. Collaborative Protégé made it possible for all the members of our team to work on the same copy of the Ontology, while maintaining the change log. Editor: Web-Protégé Recently we have moved to Web Protégé for the ease of use. Ontology Registry: NCBO BioPortal Consulted before proposing terms to add to OBI Made it easy to determine whether terms are already present in existing ontologies

17. Communities where We Can Increase NCBO Visibility Galaxy A popular Web-based tool that allows users to integrate data from a large number of resources. http://galaxy.psu.edu GenomeSpace A platform enabling one to work with multiple genomic analysis tools, seamlessly. http://www.genomespace.org/ Web services IEEE SERVICES: IEEE World Congress on Services http://www.servicescongress.org/2012/ Ontologies International Conference on Biomedical Ontology (ICBO) Formal Ontology in Information Systems (FOIS) http://www.kr-med.org/icbofois2012/

18. Suggestions & Complaints for Core NCBO Team Suggestions already addressed by the NCBO team: Web Protégé Support for Adding and Editing Axioms e.g., Adding restrictions on properties for concepts Documentation for Layout Configuration to the Wiki Additional Suggestions Web Protégé Support for Reasoning Support for Finding Term Usage Interface for Exporting and Uploading Ontologies

19. Milestones and Plans ArtifactCurrent Version Next Version Improvements OBI-WSMarch 2012Jul 2012Addition of terms for annotation of Galaxy Tools and EuPathDB Web services OBI-enriched-WSMarch 2012Jul 2012 WSDL_XSD ParserApr 2011Apr 2012Add documentation and release ConceptSim Metrics Nov 2011Jul 2012Generalize to work with multiple ontologies Galaxy WS- Extensions Jul 2011Jun 2012Add support for utilizing available semantics RadiantWebDec 2011Apr 2012Add support for WADL Web services LuminaWebNAJul 2012Developing discovery tool SSEMar 2012Jul 2012Improved use of Semantics, work with multiple Ontologies and data mediation Phylip WSNAJul 2012Developing phylogenetic service EuPathDB WSNAJul 2012Re-engineering EuPathDB services

20. Questions

21. Find Services / Tools, contd. Discovery of operations over annotated Web services: LuminaWeb <input name=“seq” /> WSDL for WUBLAST Web service Ontology Tool for : Sequence Alignment Input : protein Sequences Output : ….. Search LuminaWeb